17 Search Results for "Williams, Richard Ryan"

Document
DOI: 10.4230/LIPIcs.WABI.2024.14
A Unifying Taxonomy of Pattern Matching in Degenerate Strings and Founder Graphs

Authors: Rocco Ascone, Giulia Bernardini, Alessio Conte, Massimo Equi, Esteban Gabory, Roberto Grossi, and Nadia Pisanti

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
Elastic Degenerate (ED) strings and Elastic Founder (EF) graphs are two versions of acyclic components of pangenomes. Both ED strings and EF graphs (which we collectively name variable strings) extend the well-known notion of indeterminate string. Recent work has extensively investigated algorithmic tasks over these structures, and over several other variable strings notions that they generalise. Among such tasks, the basic operation of matching a pattern into a text, which can serve as a toolkit for many pangenomic data analyses using these data structures, deserves special attention. In this paper we: (1) highlight a clear taxonomy within both ED strings and EF graphs ranging through variable strings of all types, from the linear string up to the most general one; (2) investigate the problem PvarT(X,Y) of matching a solid or variable pattern of type X into a variable text of type Y; (3) using as a reference the quadratic conditional lower bounds that are known for PvarT(solid,ED) and PvarT(solid,EF), for all possible types of variable strings X and Y we either prove the quadratic conditional lower bound for PvarT(X,Y), or provide non-trivial, often sub-quadratic, upper bounds, also exploiting the above-mentioned taxonomy.
Cite as

Rocco Ascone, Giulia Bernardini, Alessio Conte, Massimo Equi, Esteban Gabory, Roberto Grossi, and Nadia Pisanti. A Unifying Taxonomy of Pattern Matching in Degenerate Strings and Founder Graphs. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 14:1-14:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{ascone_et_al:LIPIcs.WABI.2024.14,
  author =	{Ascone, Rocco and Bernardini, Giulia and Conte, Alessio and Equi, Massimo and Gabory, Esteban and Grossi, Roberto and Pisanti, Nadia},
  title =	{{A Unifying Taxonomy of Pattern Matching in Degenerate Strings and Founder Graphs}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{14:1--14:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.14},
  URN =		{urn:nbn:de:0030-drops-206586},
  doi =		{10.4230/LIPIcs.WABI.2024.14},
  annote =	{Keywords: Pangenomics, pattern matching, degenerate string, founder graph, fine-grained complexity}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.22
Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads

Authors: Xiaofei Carl Zang, Xiang Li, Kyle Metcalfe, Tuval Ben-Yehezkel, Ryan Kelley, and Mingfu Shao

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
Modern sequencing technologies allow for the addition of short-sequence tags, known as anchors, to both ends of a captured molecule. Anchors are useful in assembling the full-length sequence of a captured molecule as they can be used to accurately determine the endpoints. One representative of such anchor-enabled technology is LoopSeq Solo, a synthetic long read (SLR) sequencing protocol. LoopSeq Solo also achieves ultra-high sequencing depth and high purity of short reads covering the entire captured molecule. Despite the availability of many assembly methods, constructing full-length sequence from these anchor-enabled, ultra-high coverage sequencing data remains challenging due to the complexity of the underlying assembly graphs and the lack of specific algorithms leveraging anchors. We present Anchorage, a novel assembler that performs anchor-guided assembly for ultra-high-depth sequencing data. Anchorage starts with a kmer-based approach for precise estimation of molecule lengths. It then formulates the assembly problem as finding an optimal path that connects the two nodes determined by anchors in the underlying compact de Bruijn graph. The optimality is defined as maximizing the weight of the smallest node while matching the estimated sequence length. Anchorage uses a modified dynamic programming algorithm to efficiently find the optimal path. Through both simulations and real data, we show that Anchorage outperforms existing assembly methods, particularly in the presence of sequencing artifacts. Anchorage fills the gap in assembling anchor-enabled data. We anticipate its broad use as anchor-enabled sequencing technologies become prevalent. Anchorage is freely available at https://github.com/Shao-Group/anchorage; the scripts and documents that can reproduce all experiments in this manuscript are available at https://github.com/Shao-Group/anchorage-test.
Cite as

Xiaofei Carl Zang, Xiang Li, Kyle Metcalfe, Tuval Ben-Yehezkel, Ryan Kelley, and Mingfu Shao. Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 22:1-22:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{zang_et_al:LIPIcs.WABI.2024.22,
  author =	{Zang, Xiaofei Carl and Li, Xiang and Metcalfe, Kyle and Ben-Yehezkel, Tuval and Kelley, Ryan and Shao, Mingfu},
  title =	{{Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{22:1--22:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.22},
  URN =		{urn:nbn:de:0030-drops-206660},
  doi =		{10.4230/LIPIcs.WABI.2024.22},
  annote =	{Keywords: Genome assembly, de Bruijn graph, synthetic long reads, anchor-guided assembly, LoopSeq}
}
Document
DOI: 10.4230/LIPIcs.SAT.2024.24
Hierarchical Stochastic SAT and Quality Assessment of Logic Locking

Authors: Christoph Scholl, Tobias Seufert, and Fabian Siegwolf

Published in: LIPIcs, Volume 305, 27th International Conference on Theory and Applications of Satisfiability Testing (SAT 2024)

Abstract
Motivated by the application of quality assessment of logic locking we introduce Hierarchical Stochastic SAT (HSSAT) which generalizes Stochastic SAT (SSAT). We look into the complexity of HSSAT and for solving HSSAT formulas we provide a prototype solver which computes exact evaluation results (i.e., without any approximation and without any imprecision caused by numerical rounding errors). Finally, we perform an intensive experimental evaluation of our HSSAT solver in the context of quality assessment of logic locking.
Cite as

Christoph Scholl, Tobias Seufert, and Fabian Siegwolf. Hierarchical Stochastic SAT and Quality Assessment of Logic Locking. In 27th International Conference on Theory and Applications of Satisfiability Testing (SAT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 305, pp. 24:1-24:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{scholl_et_al:LIPIcs.SAT.2024.24,
  author =	{Scholl, Christoph and Seufert, Tobias and Siegwolf, Fabian},
  title =	{{Hierarchical Stochastic SAT and Quality Assessment of Logic Locking}},
  booktitle =	{27th International Conference on Theory and Applications of Satisfiability Testing (SAT 2024)},
  pages =	{24:1--24:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-334-8},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{305},
  editor =	{Chakraborty, Supratik and Jiang, Jie-Hong Roland},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAT.2024.24},
  URN =		{urn:nbn:de:0030-drops-205462},
  doi =		{10.4230/LIPIcs.SAT.2024.24},
  annote =	{Keywords: Stochastic Boolean Satisfiability, Hierarchical Stochastic SAT, Binary Decision Diagrams, Decision Procedure}
}
Document
DOI: 10.4230/LIPIcs.CCC.2024.1
A Technique for Hardness Amplification Against AC⁰

Authors: William M. Hoza

Published in: LIPIcs, Volume 300, 39th Computational Complexity Conference (CCC 2024)

Abstract
We study hardness amplification in the context of two well-known "moderate" average-case hardness results for AC⁰ circuits. First, we investigate the extent to which AC⁰ circuits of depth d can approximate AC⁰ circuits of some larger depth d + k. The case k = 1 is resolved by Håstad, Rossman, Servedio, and Tan’s celebrated average-case depth hierarchy theorem (JACM 2017). Our contribution is a significantly stronger correlation bound when k ≥ 3. Specifically, we show that there exists a linear-size AC⁰_{d + k} circuit h : {0, 1}ⁿ → {0, 1} such that for every AC⁰_d circuit g, either g has size exp(n^{Ω(1/d)}), or else g agrees with h on at most a (1/2 + ε)-fraction of inputs where ε = exp(-(1/d) ⋅ Ω(log n)^{k-1}). For comparison, Håstad, Rossman, Servedio, and Tan’s result has ε = n^{-Θ(1/d)}. Second, we consider the majority function. It is well known that the majority function is moderately hard for AC⁰ circuits (and stronger classes). Our contribution is a stronger correlation bound for the XOR of t copies of the n-bit majority function, denoted MAJ_n^{⊕ t}. We show that if g is an AC⁰_d circuit of size S, then g agrees with MAJ_n^{⊕ t} on at most a (1/2 + ε)-fraction of inputs, where ε = (O(log S)^{d - 1} / √n)^t. To prove these results, we develop a hardness amplification technique that is tailored to a specific type of circuit lower bound proof. In particular, one way to show that a function h is moderately hard for AC⁰ circuits is to (a) design some distribution over random restrictions or random projections, (b) show that AC⁰ circuits simplify to shallow decision trees under these restrictions/projections, and finally (c) show that after applying the restriction/projection, h is moderately hard for shallow decision trees with respect to an appropriate distribution. We show that (roughly speaking) if h can be proven to be moderately hard by a proof with that structure, then XORing multiple copies of h amplifies its hardness. Our analysis involves a new kind of XOR lemma for decision trees, which might be of independent interest.
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William M. Hoza. A Technique for Hardness Amplification Against AC⁰. In 39th Computational Complexity Conference (CCC 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 300, pp. 1:1-1:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{hoza:LIPIcs.CCC.2024.1,
  author =	{Hoza, William M.},
  title =	{{A Technique for Hardness Amplification Against AC⁰}},
  booktitle =	{39th Computational Complexity Conference (CCC 2024)},
  pages =	{1:1--1:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-331-7},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{300},
  editor =	{Santhanam, Rahul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2024.1},
  URN =		{urn:nbn:de:0030-drops-203977},
  doi =		{10.4230/LIPIcs.CCC.2024.1},
  annote =	{Keywords: Bounded-depth circuits, average-case lower bounds, hardness amplification, XOR lemmas}
}
Document
DOI: 10.4230/LIPIcs.CCC.2024.4
Derandomizing Logspace with a Small Shared Hard Drive

Authors: Edward Pyne

Published in: LIPIcs, Volume 300, 39th Computational Complexity Conference (CCC 2024)

Abstract
We obtain new catalytic algorithms for space-bounded derandomization. In the catalytic computation model introduced by (Buhrman, Cleve, Koucký, Loff, and Speelman STOC 2013), we are given a small worktape, and a larger catalytic tape that has an arbitrary initial configuration. We may edit this tape, but it must be exactly restored to its initial configuration at the completion of the computation. We prove that BPSPACE[S] ⊆ CSPACE[S,S²] where BPSPACE[S] corresponds to randomized space S computation, and CSPACE[S,C] corresponds to catalytic algorithms that use O(S) bits of workspace and O(C) bits of catalytic space. Previously, only BPSPACE[S] ⊆ CSPACE[S,2^O(S)] was known. In fact, we prove a general tradeoff, that for every α ∈ [1,1.5], BPSPACE[S] ⊆ CSPACE[S^α,S^(3-α)]. We do not use the algebraic techniques of prior work on catalytic computation. Instead, we develop an algorithm that branches based on if the catalytic tape is conditionally random, and instantiate this primitive in a recursive framework. Our result gives an alternate proof of the best known time-space tradeoff for BPSPACE[S], due to (Cai, Chakaravarthy, and van Melkebeek, Theory Comput. Sys. 2006). As a final application, we extend our results to solve search problems in CSPACE[S,S²]. As far as we are aware, this constitutes the first study of search problems in the catalytic computing model.
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Edward Pyne. Derandomizing Logspace with a Small Shared Hard Drive. In 39th Computational Complexity Conference (CCC 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 300, pp. 4:1-4:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{pyne:LIPIcs.CCC.2024.4,
  author =	{Pyne, Edward},
  title =	{{Derandomizing Logspace with a Small Shared Hard Drive}},
  booktitle =	{39th Computational Complexity Conference (CCC 2024)},
  pages =	{4:1--4:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-331-7},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{300},
  editor =	{Santhanam, Rahul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2024.4},
  URN =		{urn:nbn:de:0030-drops-204006},
  doi =		{10.4230/LIPIcs.CCC.2024.4},
  annote =	{Keywords: Catalytic computation, space-bounded computation, derandomization}
}
Document
DOI: 10.4230/LIPIcs.CCC.2024.35
Finer-Grained Hardness of Kernel Density Estimation

Authors: Josh Alman and Yunfeng Guan

Published in: LIPIcs, Volume 300, 39th Computational Complexity Conference (CCC 2024)

Abstract
In batch Kernel Density Estimation (KDE) for a kernel function f : ℝ^m × ℝ^m → ℝ, we are given as input 2n points x^{(1)}, …, x^{(n)}, y^{(1)}, …, y^{(n)} ∈ ℝ^m in dimension m, as well as a vector v ∈ ℝⁿ. These inputs implicitly define the n × n kernel matrix K given by K[i,j] = f(x^{(i)}, y^{(j)}). The goal is to compute a vector v ∈ ℝⁿ which approximates K w, i.e., with || Kw - v||_∞ < ε ||w||₁. For illustrative purposes, consider the Gaussian kernel f(x,y) : = e^{-||x-y||₂²}. The classic approach to this problem is the famous Fast Multipole Method (FMM), which runs in time n ⋅ O(log^m(ε^{-1})) and is particularly effective in low dimensions because of its exponential dependence on m. Recently, as the higher-dimensional case m ≥ Ω(log n) has seen more applications in machine learning and statistics, new algorithms have focused on this setting: an algorithm using discrepancy theory, which runs in time O(n / ε), and an algorithm based on the polynomial method, which achieves inverse polynomial accuracy in almost linear time when the input points have bounded square diameter B < o(log n). A recent line of work has proved fine-grained lower bounds, with the goal of showing that the "curse of dimensionality" arising in FMM is necessary assuming the Strong Exponential Time Hypothesis (SETH). Backurs et al. [NeurIPS 2017] first showed the hardness of a variety of Empirical Risk Minimization problems including KDE for Gaussian-like kernels in the case with high dimension m = Ω(log n) and large scale B = Ω(log n). Alman et al. [FOCS 2020] later developed new reductions in roughly this same parameter regime, leading to lower bounds for more general kernels, but only for very small error ε < 2^{- log^{Ω(1)} (n)}. In this paper, we refine the approach of Alman et al. to show new lower bounds in all parameter regimes, closing gaps between the known algorithms and lower bounds. For example: - In the setting where m = Clog n and B = o(log n), we prove Gaussian KDE requires n^{2-o(1)} time to achieve additive error ε < Ω(m/B)^{-m}, matching the performance of the polynomial method up to low-order terms. - In the low dimensional setting m = o(log n), we show that Gaussian KDE requires n^{2-o(1)} time to achieve ε such that log log (ε^{-1}) > ̃ Ω ((log n)/m), matching the error bound achievable by FMM up to low-order terms. To our knowledge, no nontrivial lower bound was previously known in this regime. Our approach also generalizes to any parameter regime and any kernel. For example, we achieve similar fine-grained hardness results for any kernel with slowly-decaying Taylor coefficients such as the Cauchy kernel. Our new lower bounds make use of an intricate analysis of the "counting matrix", a special case of the kernel matrix focused on carefully-chosen evaluation points. As a key technical lemma, we give a novel approach to bounding the entries of its inverse by using Schur polynomials from algebraic combinatorics.
Cite as

Josh Alman and Yunfeng Guan. Finer-Grained Hardness of Kernel Density Estimation. In 39th Computational Complexity Conference (CCC 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 300, pp. 35:1-35:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{alman_et_al:LIPIcs.CCC.2024.35,
  author =	{Alman, Josh and Guan, Yunfeng},
  title =	{{Finer-Grained Hardness of Kernel Density Estimation}},
  booktitle =	{39th Computational Complexity Conference (CCC 2024)},
  pages =	{35:1--35:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-331-7},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{300},
  editor =	{Santhanam, Rahul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2024.35},
  URN =		{urn:nbn:de:0030-drops-204311},
  doi =		{10.4230/LIPIcs.CCC.2024.35},
  annote =	{Keywords: Kernel Density Estimation, Fine-Grained Complexity, Schur Polynomials}
}
Document
DOI: 10.4230/LIPIcs.CCC.2024.36
Gap MCSP Is Not (Levin) NP-Complete in Obfustopia

Authors: Noam Mazor and Rafael Pass

Published in: LIPIcs, Volume 300, 39th Computational Complexity Conference (CCC 2024)

Abstract
We demonstrate that under believable cryptographic hardness assumptions, Gap versions of standard meta-complexity problems, such as the Minimum Circuit Size Problem (MCSP) and the Minimum Time-Bounded Kolmogorov Complexity problem (MKTP) are not NP-complete w.r.t. Levin (i.e., witness-preserving many-to-one) reductions. In more detail: - Assuming the existence of indistinguishability obfuscation, and subexponentially-secure one-way functions, an appropriate Gap version of MCSP is not NP-complete under randomized Levin-reductions. - Assuming the existence of subexponentially-secure indistinguishability obfuscation, subexponentially-secure one-way functions and injective PRGs, an appropriate Gap version of MKTP is not NP-complete under randomized Levin-reductions.
Cite as

Noam Mazor and Rafael Pass. Gap MCSP Is Not (Levin) NP-Complete in Obfustopia. In 39th Computational Complexity Conference (CCC 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 300, pp. 36:1-36:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{mazor_et_al:LIPIcs.CCC.2024.36,
  author =	{Mazor, Noam and Pass, Rafael},
  title =	{{Gap MCSP Is Not (Levin) NP-Complete in Obfustopia}},
  booktitle =	{39th Computational Complexity Conference (CCC 2024)},
  pages =	{36:1--36:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-331-7},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{300},
  editor =	{Santhanam, Rahul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2024.36},
  URN =		{urn:nbn:de:0030-drops-204322},
  doi =		{10.4230/LIPIcs.CCC.2024.36},
  annote =	{Keywords: Kolmogorov complexity, MCSP, Levin Reduction}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.15
Determining Fixed-Length Paths in Directed and Undirected Edge-Weighted Graphs

Authors: Daniel Hambly, Rhyd Lewis, and Padraig Corcoran

Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)

Abstract
In this paper, we examine the NP-hard problem of identifying fixed-length s-t paths in edge-weighted graphs - that is, a path of a desired length k from a source vertex s to a target vertex t. Many existing strategies look at paths whose lengths are determined by the number of edges in the path. We, however, look at the length of the path as the sum of the edge weights. Here, three exact algorithms for this problem are proposed: the first based on an integer programming (IP) formulation, the second a backtracking algorithm, and the third based on an extension of Yen’s algorithm. Analysis of these algorithms on random graphs shows that the backtracking algorithm performs best on smaller values of k, whilst the IP is preferable for larger values of k.
Cite as

Daniel Hambly, Rhyd Lewis, and Padraig Corcoran. Determining Fixed-Length Paths in Directed and Undirected Edge-Weighted Graphs. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 15:1-15:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{hambly_et_al:LIPIcs.SEA.2024.15,
  author =	{Hambly, Daniel and Lewis, Rhyd and Corcoran, Padraig},
  title =	{{Determining Fixed-Length Paths in Directed and Undirected Edge-Weighted Graphs}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{15:1--15:11},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-325-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{301},
  editor =	{Liberti, Leo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.15},
  URN =		{urn:nbn:de:0030-drops-203805},
  doi =		{10.4230/LIPIcs.SEA.2024.15},
  annote =	{Keywords: Graphs, paths, backtracking, integer programming, Yen’s algorithm}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2024.7
Finer-Grained Reductions in Fine-Grained Hardness of Approximation

Authors: Elie Abboud and Noga Ron-Zewi

Published in: LIPIcs, Volume 297, 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)

Abstract
We investigate the relation between δ and ε required for obtaining a (1+δ)-approximation in time N^{2-ε} for closest pair problems under various distance metrics, and for other related problems in fine-grained complexity. Specifically, our main result shows that if it is impossible to (exactly) solve the (bichromatic) inner product (IP) problem for vectors of dimension c log N in time N^{2-ε}, then there is no (1+δ)-approximation algorithm for (bichromatic) Euclidean Closest Pair running in time N^{2-2ε}, where δ ≈ (ε/c)² (where ≈ hides polylog factors). This improves on the prior result due to Chen and Williams (SODA 2019) which gave a smaller polynomial dependence of δ on ε, on the order of δ ≈ (ε/c)⁶. Our result implies in turn that no (1+δ)-approximation algorithm exists for Euclidean closest pair for δ ≈ ε⁴, unless an algorithmic improvement for IP is obtained. This in turn is very close to the approximation guarantee of δ ≈ ε³ for Euclidean closest pair, given by the best known algorithm of Almam, Chan, and Williams (FOCS 2016). By known reductions, a similar result follows for a host of other related problems in fine-grained hardness of approximation. Our reduction combines the hardness of approximation framework of Chen and Williams, together with an MA communication protocol for IP over a small alphabet, that is inspired by the MA protocol of Chen (Theory of Computing, 2020).
Cite as

Elie Abboud and Noga Ron-Zewi. Finer-Grained Reductions in Fine-Grained Hardness of Approximation. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 7:1-7:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{abboud_et_al:LIPIcs.ICALP.2024.7,
  author =	{Abboud, Elie and Ron-Zewi, Noga},
  title =	{{Finer-Grained Reductions in Fine-Grained Hardness of Approximation}},
  booktitle =	{51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)},
  pages =	{7:1--7:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-322-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{297},
  editor =	{Bringmann, Karl and Grohe, Martin and Puppis, Gabriele and Svensson, Ola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2024.7},
  URN =		{urn:nbn:de:0030-drops-201507},
  doi =		{10.4230/LIPIcs.ICALP.2024.7},
  annote =	{Keywords: Fine-grained complexity, conditional lower bound, fine-grained reduction, Approximation algorithms, Analysis of algorithms, Computational geometry, Computational and structural complexity theory}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2024.22
Two-Sets Cut-Uncut on Planar Graphs

Authors: Matthias Bentert, Pål Grønås Drange, Fedor V. Fomin, Petr A. Golovach, and Tuukka Korhonen

Published in: LIPIcs, Volume 297, 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)

Abstract
We study Two-Sets Cut-Uncut on planar graphs. Therein, one is given an undirected planar graph G and two disjoint sets S and T of vertices as input. The question is, what is the minimum number of edges to remove from G, such that all vertices in S are separated from all vertices in T, while maintaining that every vertex in S, and respectively in T, stays in the same connected component. We show that this problem can be solved in 2^{|S|+|T|} n^𝒪(1) time with a one-sided-error randomized algorithm. Our algorithm implies a polynomial-time algorithm for the network diversion problem on planar graphs, which resolves an open question from the literature. More generally, we show that Two-Sets Cut-Uncut is fixed-parameter tractable when parameterized by the number r of faces in a planar embedding covering the terminals S ∪ T, by providing a 2^𝒪(r) n^𝒪(1)-time algorithm.
Cite as

Matthias Bentert, Pål Grønås Drange, Fedor V. Fomin, Petr A. Golovach, and Tuukka Korhonen. Two-Sets Cut-Uncut on Planar Graphs. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 22:1-22:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bentert_et_al:LIPIcs.ICALP.2024.22,
  author =	{Bentert, Matthias and Drange, P\r{a}l Gr{\o}n\r{a}s and Fomin, Fedor V. and Golovach, Petr A. and Korhonen, Tuukka},
  title =	{{Two-Sets Cut-Uncut on Planar Graphs}},
  booktitle =	{51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)},
  pages =	{22:1--22:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-322-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{297},
  editor =	{Bringmann, Karl and Grohe, Martin and Puppis, Gabriele and Svensson, Ola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2024.22},
  URN =		{urn:nbn:de:0030-drops-201654},
  doi =		{10.4230/LIPIcs.ICALP.2024.22},
  annote =	{Keywords: planar graphs, cut-uncut, group-constrained paths}
}
Document
DOI: 10.4230/LIPIcs.STACS.2024.25
Depth-3 Circuit Lower Bounds for k-OV

Authors: Tameem Choudhury and Karteek Sreenivasaiah

Published in: LIPIcs, Volume 289, 41st International Symposium on Theoretical Aspects of Computer Science (STACS 2024)

Abstract
The 2-Orthogonal Vectors (2-OV) problem is the following: given two tuples A and B of n Boolean vectors, each of dimension d, decide if there exist vectors u ∈ A, and v ∈ B, such that u and v are orthogonal. This problem, and its generalization k-OV defined analogously for k tuples, are central problems in the area of fine-grained complexity. One of the major conjectures in fine-grained complexity is that k-OV cannot be solved by a randomised algorithm in n^{k-ε}poly(d) time for any constant ε > 0. In this paper, we are interested in unconditional lower bounds against k-OV, but for weaker models of computation than the general Turing Machine. In particular, we are interested in circuit lower bounds to computing k-OV by Boolean circuit families of depth 3 of the form OR-AND-OR, or equivalently, a disjunction of CNFs. We show that for all k ≤ d, any disjunction of t-CNFs computing k-OV requires size Ω((n/t)^k). In particular, when k is a constant, any disjunction of k-CNFs computing k-OV needs to use Ω(n^k) CNFs. This matches the brute-force construction, and for each fixed k > 2, this is the first unconditional Ω(n^k) lower bound against k-OV for a computation model that can compute it in size O(n^k). Our results partially resolve a conjecture by Kane and Williams [Daniel M. Kane and Richard Ryan Williams, 2019] (page 12, conjecture 10) about depth-3 AC⁰ circuits computing 2-OV. As a secondary result, we show an exponential lower bound on the size of AND∘OR∘AND circuits computing 2-OV when d is very large. Since 2-OV reduces to k-OV by projections trivially, this lower bound works against k-OV as well.
Cite as

Tameem Choudhury and Karteek Sreenivasaiah. Depth-3 Circuit Lower Bounds for k-OV. In 41st International Symposium on Theoretical Aspects of Computer Science (STACS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 289, pp. 25:1-25:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{choudhury_et_al:LIPIcs.STACS.2024.25,
  author =	{Choudhury, Tameem and Sreenivasaiah, Karteek},
  title =	{{Depth-3 Circuit Lower Bounds for k-OV}},
  booktitle =	{41st International Symposium on Theoretical Aspects of Computer Science (STACS 2024)},
  pages =	{25:1--25:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-311-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{289},
  editor =	{Beyersdorff, Olaf and Kant\'{e}, Mamadou Moustapha and Kupferman, Orna and Lokshtanov, Daniel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2024.25},
  URN =		{urn:nbn:de:0030-drops-197359},
  doi =		{10.4230/LIPIcs.STACS.2024.25},
  annote =	{Keywords: fine grained complexity, k-OV, circuit lower bounds, depth-3 circuits}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2019.48
The Orthogonal Vectors Conjecture for Branching Programs and Formulas

Authors: Daniel M. Kane and Richard Ryan Williams

Published in: LIPIcs, Volume 124, 10th Innovations in Theoretical Computer Science Conference (ITCS 2019)

Abstract
In the Orthogonal Vectors (OV) problem, we wish to determine if there is an orthogonal pair of vectors among n Boolean vectors in d dimensions. The OV Conjecture (OVC) posits that OV requires n^{2-o(1)} time to solve, for all d=omega(log n). Assuming the OVC, optimal time lower bounds have been proved for many prominent problems in P, such as Edit Distance, Frechet Distance, Longest Common Subsequence, and approximating the diameter of a graph. We prove that OVC is true in several computational models of interest: - For all sufficiently large n and d, OV for n vectors in {0,1}^d has branching program complexity Theta~(n * min(n,2^d)). In particular, the lower and upper bounds match up to polylog factors. - OV has Boolean formula complexity Theta~(n * min(n,2^d)), over all complete bases of O(1) fan-in. - OV requires Theta~(n * min(n,2^d)) wires, in formulas comprised of gates computing arbitrary symmetric functions of unbounded fan-in. Our lower bounds basically match the best known (quadratic) lower bounds for any explicit function in those models. Analogous lower bounds hold for many related problems shown to be hard under OVC, such as Batch Partial Match, Batch Subset Queries, and Batch Hamming Nearest Neighbors, all of which have very succinct reductions to OV. The proofs use a certain kind of input restriction that is different from typical random restrictions where variables are assigned independently. We give a sense in which independent random restrictions cannot be used to show hardness, in that OVC is false in the "average case" even for AC^0 formulas: For all p in (0,1) there is a delta_p > 0 such that for every n and d, OV instances with input bits independently set to 1 with probability p (and 0 otherwise) can be solved with AC^0 formulas of O(n^{2-delta_p}) size, on all but a o_n(1) fraction of instances. Moreover, lim_{p - > 1}delta_p = 1.
Cite as

Daniel M. Kane and Richard Ryan Williams. The Orthogonal Vectors Conjecture for Branching Programs and Formulas. In 10th Innovations in Theoretical Computer Science Conference (ITCS 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 124, pp. 48:1-48:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{kane_et_al:LIPIcs.ITCS.2019.48,
  author =	{Kane, Daniel M. and Williams, Richard Ryan},
  title =	{{The Orthogonal Vectors Conjecture for Branching Programs and Formulas}},
  booktitle =	{10th Innovations in Theoretical Computer Science Conference (ITCS 2019)},
  pages =	{48:1--48:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-095-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{124},
  editor =	{Blum, Avrim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2019.48},
  URN =		{urn:nbn:de:0030-drops-101418},
  doi =		{10.4230/LIPIcs.ITCS.2019.48},
  annote =	{Keywords: fine-grained complexity, orthogonal vectors, branching programs, symmetric functions, Boolean formulas}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2019.56
Quadratic Time-Space Lower Bounds for Computing Natural Functions with a Random Oracle

Authors: Dylan M. McKay and Richard Ryan Williams

Published in: LIPIcs, Volume 124, 10th Innovations in Theoretical Computer Science Conference (ITCS 2019)

Abstract
We define a model of size-S R-way branching programs with oracles that can make up to S distinct oracle queries over all of their possible inputs, and generalize a lower bound proof strategy of Beame [SICOMP 1991] to apply in the case of random oracles. Through a series of succinct reductions, we prove that the following problems require randomized algorithms where the product of running time and space usage must be Omega(n^2/poly(log n)) to obtain correct answers with constant nonzero probability, even for algorithms with constant-time access to a uniform random oracle (i.e., a uniform random hash function): - Given an unordered list L of n elements from [n] (possibly with repeated elements), output [n]-L. - Counting satisfying assignments to a given 2CNF, and printing any satisfying assignment to a given 3CNF. Note it is a major open problem to prove a time-space product lower bound of n^{2-o(1)} for the decision version of SAT, or even for the decision problem Majority-SAT. - Printing the truth table of a given CNF formula F with k inputs and n=O(2^k) clauses, with values printed in lexicographical order (i.e., F(0^k), F(0^{k-1}1), ..., F(1^k)). Thus we have a 4^k/poly(k) lower bound in this case. - Evaluating a circuit with n inputs and O(n) outputs. As our lower bounds are based on R-way branching programs, they hold for any reasonable model of computation (e.g. log-word RAMs and multitape Turing machines).
Cite as

Dylan M. McKay and Richard Ryan Williams. Quadratic Time-Space Lower Bounds for Computing Natural Functions with a Random Oracle. In 10th Innovations in Theoretical Computer Science Conference (ITCS 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 124, pp. 56:1-56:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{mckay_et_al:LIPIcs.ITCS.2019.56,
  author =	{McKay, Dylan M. and Williams, Richard Ryan},
  title =	{{Quadratic Time-Space Lower Bounds for Computing Natural Functions with a Random Oracle}},
  booktitle =	{10th Innovations in Theoretical Computer Science Conference (ITCS 2019)},
  pages =	{56:1--56:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-095-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{124},
  editor =	{Blum, Avrim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2019.56},
  URN =		{urn:nbn:de:0030-drops-101493},
  doi =		{10.4230/LIPIcs.ITCS.2019.56},
  annote =	{Keywords: branching programs, random oracles, time-space tradeoffs, lower bounds, SAT, counting complexity}
}
Document
Invited Paper
DOI: 10.4230/LIPIcs.ICALP.2018.4
Lower Bounds by Algorithm Design: A Progress Report (Invited Paper)

Authors: Richard Ryan Williams

Published in: LIPIcs, Volume 107, 45th International Colloquium on Automata, Languages, and Programming (ICALP 2018)

Abstract
In 2010, the author proposed a program for proving lower bounds in circuit complexity, via faster algorithms for circuit satisfiability and related problems. This talk will give an overview of how the program works, report on the successes of this program so far, and outline open frontiers that have yet to be resolved.
Cite as

Richard Ryan Williams. Lower Bounds by Algorithm Design: A Progress Report (Invited Paper). In 45th International Colloquium on Automata, Languages, and Programming (ICALP 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 107, p. 4:1, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{williams:LIPIcs.ICALP.2018.4,
  author =	{Williams, Richard Ryan},
  title =	{{Lower Bounds by Algorithm Design: A Progress Report}},
  booktitle =	{45th International Colloquium on Automata, Languages, and Programming (ICALP 2018)},
  pages =	{4:1--4:1},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-076-7},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{107},
  editor =	{Chatzigiannakis, Ioannis and Kaklamanis, Christos and Marx, D\'{a}niel and Sannella, Donald},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2018.4},
  URN =		{urn:nbn:de:0030-drops-90088},
  doi =		{10.4230/LIPIcs.ICALP.2018.4},
  annote =	{Keywords: circuit complexity, satisfiability, derandomization}
}
Document
DOI: 10.4230/LIPIcs.CCC.2018.6
Limits on Representing Boolean Functions by Linear Combinations of Simple Functions: Thresholds, ReLUs, and Low-Degree Polynomials

Authors: Richard Ryan Williams

Published in: LIPIcs, Volume 102, 33rd Computational Complexity Conference (CCC 2018)

Abstract
We consider the problem of representing Boolean functions exactly by "sparse" linear combinations (over R) of functions from some "simple" class C. In particular, given C we are interested in finding low-complexity functions lacking sparse representations. When C forms a basis for the space of Boolean functions (e.g., the set of PARITY functions or the set of conjunctions) this sort of problem has a well-understood answer; the problem becomes interesting when C is "overcomplete" and the set of functions is not linearly independent. We focus on the cases where C is the set of linear threshold functions, the set of rectified linear units (ReLUs), and the set of low-degree polynomials over a finite field, all of which are well-studied in different contexts. We provide generic tools for proving lower bounds on representations of this kind. Applying these, we give several new lower bounds for "semi-explicit" Boolean functions. Let alpha(n) be an unbounded function such that n^{alpha(n)} is time constructible (e.g. alpha(n) = log^*(n)). We show: - Functions in NTIME[n^{alpha(n)}] that require super-polynomially many linear threshold functions to represent (depth-two neural networks with sign activation function, a special case of depth-two threshold circuit lower bounds). - Functions in NTIME[n^{alpha(n)}] that require super-polynomially many ReLU gates to represent (depth-two neural networks with ReLU activation function). - Functions in NTIME[n^{alpha(n)}] that require super-polynomially many O(1)-degree F_p-polynomials to represent exactly, for every prime p (related to problems regarding Higher-Order "Uncertainty Principles"). We also obtain a function in E^{NP} requiring 2^{Omega(n)} linear combinations. - Functions in NTIME[n^{poly(log n)}] that require super-polynomially many ACC ° THR circuits to represent exactly (further generalizing the recent lower bounds of Murray and the author). We also obtain "fixed-polynomial" lower bounds for functions in NP, for the first three representation classes. All our lower bounds are obtained via algorithms for analyzing linear combinations of simple functions in the above scenarios, in ways which substantially beat exhaustive search.
Cite as

Richard Ryan Williams. Limits on Representing Boolean Functions by Linear Combinations of Simple Functions: Thresholds, ReLUs, and Low-Degree Polynomials. In 33rd Computational Complexity Conference (CCC 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 102, pp. 6:1-6:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{williams:LIPIcs.CCC.2018.6,
  author =	{Williams, Richard Ryan},
  title =	{{Limits on Representing Boolean Functions by Linear Combinations of Simple Functions: Thresholds, ReLUs, and Low-Degree Polynomials}},
  booktitle =	{33rd Computational Complexity Conference (CCC 2018)},
  pages =	{6:1--6:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-069-9},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{102},
  editor =	{Servedio, Rocco A.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2018.6},
  URN =		{urn:nbn:de:0030-drops-88846},
  doi =		{10.4230/LIPIcs.CCC.2018.6},
  annote =	{Keywords: linear threshold functions, lower bounds, neural networks, low-degree polynomials}
}
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